Structure of PDB 8dl2 Chain A

Receptor sequence

>8dl2A (length=712) Species: 411476 (Bacteroides ovatus ATCC 8483)

VLHDGFNFDPAIPKADEPLTITFKAPEGSNFYGYADDLYLHSGTGANWTG
APTWGDNQNKYRLKKTKDNVWSITLSSSIRHFYSVAPSTPLQTINLIVRD
AEGSQQTYDYATLVEDSQNGFIWEEPQKAPLPISGEEKEGIHIHSATSIM
LVLYDKDSQGGHKDCVFVTGNFNNWKLDSRYMMKYDETNHCWWITLEELT
AGETQFQYFVYSASDGGTYLCDPYCEQALEKGVDTNFPTGAQAPYVSVVS
TNPQPYQWSAGEFEMKNKENPVIYELLLRDFTSSGNLAGAMEKLPYLKEL
GIDAIELMPVQEFAGNDSWGYNTGLYFALDASYGTQNEYKAFIDACHQNG
IAVIFDVVYNHTNNDNPFARMYWDTFNNRPSTKNPWLNAVTPHQKYVFSP
DDFNHTSEQTKAFVKRNLKYLLDTYHIDGFRFDFTKGFTQKQTTGDDDLA
ATDPARVSVLKEYYEAVKAVKEDAMVTMEHFCANEETTLATEGIHFWRNM
NHSYCQSAMGWKDNSDFSGLYDTTRPNQFVGYMESHDEERCAYKQIEYGN
GALKTNLSERLKQLSSNAAFFFTVPGPKMLWQFGEMGYDISIDENGRTGK
KPVLWEYQTERKSLVDIYTKLITLRTTHSDLFNASSQFTWKVSYNDWDNG
RTLTLKAVNGKQLHVYANFTNASIDYTIPEGTWYLYLEGNPVEGEKKISV
PAHEFRLYTNFA

3D structure

• PDB: 8dl2 BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut.
• Chain: A
• Resolution: 1.99 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	GLC	A	H85 W98 Q150	H41 W54 Q106
BS02	AC1	A	H85 W92 D153	H41 W48 D109
BS03	GLC	A	K588 Y592	K544 Y548
BS04	AC1	A	Q550 W555 D557 Y592	Q506 W511 D513 Y548
BS05	GLC	A	F525 N543	F481 N499
BS06	AC1	A	W363 Y365 F442 D477 F478 E523 H580 D581	W319 Y321 F398 D433 F434 E479 H536 D537
BS07	GLC	A	W363 Y365 R641	W319 Y321 R597
BS08	CA	A	E274 E356 F357 G359 D374	E230 E312 F313 G315 D330
BS09	MN	A	N404 H437 D446 G481	N360 H393 D402 G437

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 22 19:29:19 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()

   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1444         else:

=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1446     

   1447     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '8dl2', asym_id = 'A', title = 'BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='8dl2', asym_id='A', title='BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.')

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0005975', uniprot = '', pdbid = '8dl2', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005975', uniprot='', pdbid='8dl2', asym_id='A')

    480         '''.replace("$namespace_link",namespace_link

    481           ).replace("$namespace",namespace

=>  482           ).replace("$uniprot",u

    483         ))

    484         for l,(term,name) in enumerate(go2aspect[Aspect]):

u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>